Re: [galaxy-dev] error installing dependency for tool shed repository.

21 Aug 2013

      Curt,

I'm happy to hear that everything is now working. If you encounter any 
further issues, please don't hesitate to contact us.

  --Dave B.

On 2013-08-21 21:31, Curt Palm wrote:
...
Hi Dave,
I made changes giving the suggestions of Ross, I got a different error and
that gave me insight as to what was going on.  I uploaded new xml:
<?xml version="1.0"?>
<tool_dependency>
     <package name="requests" version="1.2.3">
         <install version="1.0">
             <actions>
                 <action
type="download_by_url">http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz</action>
                 <action
type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">export
PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
                 python setup.py install --home $INSTALL_DIR
--install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">
                     <environment_variable name="PYTHONPATH"
action="append_to">$INSTALL_DIR/lib/python</environment_variable>
                     <environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
</actions>
         </install>
         <readme>
         </readme>
     </package>
</tool_dependency>
And this worked for me.   I'm thinking you may have downloaded after I
made the changes.
-Curt
On 8/21/13 6:01 PM, "Dave Bouvier" <dave@bx.psu.edu> wrote:
...
Curt,
I tried installing the ingtest repository on a local instance of Galaxy,
and the requests python module installed without errors. Which revision
of Galaxy are you trying to install this repository into, and what kind
of environment are you running on that system?
--Dave B.
Try moving the <action
type="download_by_url">http://pypi.python.org/packages/source/r/requests/re
quests-1.2.3.tar.gz</action>
line so it's the one before
<action type="shell_command">python setup.py install --home $INSTALL_DIR
--install-scripts $INSTALL_DIR/bin</action>
I think I've been bitten by this - it seems download_by_url changes the
current path but only temporarily so you need to run setup.py immediately
as the next step?
If this works, please confirm to the entire list - I'm sending this to you
just in case I'm full of it :)
On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm <cpalm@ingenuity.com> wrote:
I've just created a repository  in the sandbox and have been trying to
test the installation of  a dependency my tool needs.  The tool needs the
python module "requests"  and I've written code. I get an error:
STDERR
python: can't open file 'setup.py': [Errno 2] No such file or directory
I've modeled my code on examples I've found in the tool shed.   I've
replaced the requests module with other python  modules and these are
installed ok.   I can also  download and  manually install requests with
"python setup.py install"
Any suggestions as to what I may be doing wrong?